Two kinds of dimethylpolysiloxane, KF-6001 and X-22-176-DX, were used to modify polyurethane. The effects of KF-6001 and X-22-176-DX on the colloidal, physico-chemical and surface properties were studied for polydimethylsiloxane modified cationic waterborne polyurethanes (SiCWPUs). The chemical structures and the surface morphologies of the SiCWPUs are characterized via Fourier transform infrared spectrometry and scanning electron microscopy. The results showed that the addition of siloxane changes the structure and surface morphology of the polyurethane. The element distributions in the polymer films were tested via X-ray photoelectron spectroscopy, and the effect of the hydrophobicity of the surfaces of the polymer films of the cationic waterborne polyurethanes was demonstrated via water contact angle tests on the surfaces of the films. As the amount of siloxane added increases, the silicon content on the surfaces of the SiCPWU1 films increases from 0% to 17.92%, and the actual silicon content on the surfaces of the films was much larger than the theoretical value. Therefore, the hydrophobicity of the membrane surface increases sharply, and the contact angle increases from 63.0° to 105.3°. Dynamic mechanical analysis indicates that the introduction of polydimethylsiloxane into the cationic aqueous polyurethane chain increases microphase separation in the polymer films. Stress–strain data showed that the mechanical properties of SiCPWU1 films were better than those of SiCPWU2 films when the same amounts of PDMS were added.